adding falcon (#5057)

* py-networkx: adding older version py-networkx

* py-pypeflow: new package

* falcon: adding new package
pacbio-daligner: adding new package
pacbio-damasker: adding new package
pacbio-dazz-db: adding new package
pacbio-dextractor: adding new package

* py-networkx: modifying version order to be in line with convention

* falcon: tweaking py-networkx dependency to satisfy setuptools
py-pypeflow: adding missing dependency

* pacbio-dextractor: changing hdf5 dependency

* pacbio-daligner: adding gmake build dep
pacbio-damasker: adding gmake build dep
pacbio-dazz-db: adding gmake build dep
pacbio-dextractor: adding gmake build dep
This commit is contained in:
snehring 2017-08-11 17:26:20 -05:00 committed by Adam J. Stewart
parent 9e7917f7d3
commit 64a32ea1f9
7 changed files with 293 additions and 0 deletions

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##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class Falcon(PythonPackage):
"""Falcon: a set of tools for fast aligning long reads for consensus
and assembly.
The Falcon tool kit is a set of simple code collection which I use
for studying efficient assembly algorithm for haploid and diploid genomes.
It has some back-end code implemented in C for speed and some simple
front-end written in Python for convenience."""
homepage = "https://github.com/PacificBiosciences/FALCON"
url = "https://github.com/PacificBiosciences/FALCON.git"
version('2017-05-30',
git='https://github.com/PacificBiosciences/FALCON.git',
commit='86cec6157291679095ea6080b0cde6561eccc041')
depends_on('py-setuptools', type='run')
depends_on('py-pypeflow', type='run')
depends_on('py-networkx@1.7:1.10', type=['build', 'run'])
depends_on('pacbio-dazz-db', type='run')
depends_on('pacbio-daligner', type='run')
depends_on('pacbio-dextractor', type='run')
depends_on('pacbio-damasker', type='run')

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##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class PacbioDaligner(MakefilePackage):
"""Daligner: The Dazzler "Overlap" Module. This is a special fork
required for some pacbio utilities."""
homepage = "https://github.com/PacificBiosciences/DALIGNER"
url = "https://github.com/PacificBiosciences/DALIGNER"
version('2017-08-05',
git='https://github.com/PacificBiosciences/DALIGNER.git',
commit='0fe5240d2cc6b55bf9e04465b700b76110749c9d')
depends_on('gmake', type='build')
depends_on('pacbio-dazz-db')
def edit(self, spec, prefix):
mkdir(prefix.bin)
makefile = FileFilter('Makefile')
makefile.filter('DEST_DIR\s*=\s*~/bin', 'DEST_DIR = ' + prefix.bin)
gmf = FileFilter('GNUmakefile')
gmf.filter('rsync\s*-av\s*\$\{ALL\}\s*\$\{PREFIX\}/bin',
'cp ${ALL} ' + prefix.bin)

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##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class PacbioDamasker(MakefilePackage):
"""Damasker: The Dazzler Repeat Masking Suite. This is a special fork
required for some pacbio utilities."""
homepage = "https://github.com/PacificBiosciences/DAMASKER"
url = "https://github.com/PacificBiosciences/DAMASKER"
version('2017-02-11',
git='https://github.com/PacificBiosciences/DAMASKER.git',
commit='144244b77d52cb785cb1b3b8ae3ab6f3f0c63264')
depends_on('gmake', type='build')
def edit(self, spec, prefix):
mkdirp(prefix.bin)
makefile = FileFilter('Makefile')
makefile.filter('DEST_DIR\s*=\s*~/bin', 'DEST_DIR = ' + prefix.bin)
gmf = FileFilter('GNUmakefile')
gmf.filter('rsync\s*-av\s*\$\{ALL\}\s*\$\{PREFIX\}/bin',
'cp ${ALL} ' + prefix.bin)

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##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class PacbioDazzDb(MakefilePackage):
"""The Dazzler Database Library. This version is a special fork
required for some pacbio utilities."""
homepage = "https://github.com/PacificBiosciences/DAZZ_DB"
url = "https://github.com/PacificBiosciences/DAZZ_DB"
version('2017-04-10',
git='https://github.com/PacificBiosciences/DAZZ_DB.git',
commit='f29d27d51f460563481cd227d17f4bdc5e288365')
depends_on('gmake', type='build')
def edit(self, spec, prefix):
mkdirp(prefix.bin)
mkdirp(prefix.lib)
mkdirp(prefix.include)
makefile = FileFilter('Makefile')
makefile.filter('DEST_DIR\s*=\s*~/bin', 'DEST_DIR = ' + prefix.bin)
gmf = FileFilter('GNUmakefile')
gmf.filter('rsync\s*-av\s*\$\{ALL\}\s*\$\{PREFIX\}/bin',
'cp ${ALL} ' + prefix.bin)
gmf.filter('rsync\s*-av\s*libdazzdb.*\s*\$\{PREFIX\}/lib',
'cp libdazzdb.* ' + prefix.lib)
gmf.filter(('rsync\s*-av\s*\$\(wildcard\s*\$\{THISDIR\}/\*.h'
'\)\s*\$\{PREFIX\}/include'),
'cp *.h ' + prefix.include)

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##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class PacbioDextractor(MakefilePackage):
"""The Dextractor and Compression Command Library. This is a special
fork required by some pacbio utilities."""
homepage = "https://github.com/PacificBiosciences/DEXTRACTOR"
url = "https://github.com/PacificBiosciences/DEXTRACTOR"
version('2016-08-09',
git='https://github.com/PacificBiosciences/DEXTRACTOR.git',
commit='89726800346d0bed15d98dcc577f4c7733aab4b1')
depends_on('hdf5')
depends_on('gmake', type='build')
def edit(self, spec, prefix):
mkdirp(prefix.bin)
makefile = FileFilter('Makefile')
makefile.filter('PATH_HDF5\s*=\s*/sw/apps/hdf5/current',
'PATH_HDF5 = ' + spec['hdf5'].prefix)
makefile.filter('PATH_HDF5\*s=\s*/usr/local/hdf5', '')
makefile.filter('DEST_DIR\s*=\s*~/bin', 'DEST_DIR = ' + prefix.bin)
gmf = FileFilter('GNUmakefile')
gmf.filter('rsync\s*-av\s*\$\{ALL\}\s*\$\{PREFIX\}/bin',
'cp ${ALL} ' + prefix.bin)

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@ -32,6 +32,7 @@ class PyNetworkx(PythonPackage):
url = "https://pypi.io/packages/source/n/networkx/networkx-1.11.tar.gz"
version('1.11', '6ef584a879e9163013e9a762e1cf7cd1')
version('1.10', 'eb7a065e37250a4cc009919dacfe7a9d')
depends_on('py-decorator', type=('build', 'run'))
depends_on('py-setuptools', type='build')

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##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class PyPypeflow(PythonPackage):
"""pypeFLOW is light weight and reusable make / flow data process
library written in Python."""
homepage = "https://github.com/PacificBiosciences/pypeFLOW"
url = "https://github.com/PacificBiosciences/pypeFLOW"
version('2017-05-04',
git='https://github.com/PacificBiosciences/pypeFLOW.git',
commit='f23a1b290876bbdf130611000934ae4247158073')
depends_on('py-setuptools', type='build')
depends_on('py-networkx@1.7:1.11', type=['build', 'run'])